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Ancient Himalayan DNA uncovered in Chicago

An international team of scientists used supercomputers in Chicago to analyze genetic material from ancient Himalayan dwellers. With high-performance computation, science is reaching new heights.

Speed read

International team collaborates to solve Himalayan origin mystery.

Sequencing and analysis used supercomputers at the University of Chicago.

Study points to genetic continuity among ancient and modern Himalayan residents.

The Himalayan mountains: Sublime wonders of the natural world. Their name alone conjures a sense of isolation, enormity, and terrifying adventure. Mt. Everest lives here, as do eight of the world's ten largest peaks.

Because of its remote location and challenging living conditions, the East Asian highlands was one of the last places on our globe to be populated by humans. Where did these hardy humans hail from?

Using supercomputers nearly as formidable as these terrific peaks, researchers conducted the first ancient DNA investigation of the Himalayan humans.

High places

Spanning 1,500 miles (2,400 kilometers) and reaching 29,029 foot (8,848 meters) at their highest point, the Himalayan mountain range presents an almost insurmountable barrier to human expansion. The surrounding high altitude valleys have long served as trade and exchange lines, yet little was known about the region’s early population history – until now.

“We demonstrate that the Himalayan mountain region was colonized by East Asians of high altitude origin, followed by millennia of genetic stability despite marked changes in material culture and mortuary behavior,” says Christina Warinner, senior author and professor in the department of anthropology at the University of Oklahoma.

Warinner and her team sought this answer because the origin of the Himalayan populations has long remained a mystery. Before her study, scientists assumed the modern Himalayan population descended from either (a) pre-historic inhabitants of the high Himalayas, or, due to challenging archaeological and osteological evidence, from (b) areas other than the Tibetan plateau. Warinner’s team decided that genetic analysis would find the answer.

“Ancient DNA has the power to reveal aspects of population history that are very difficult to infer from modern populations or archaeological material culture alone,” says study co-author Mark Aldenderfer of the University of California, Merced.

Gearing up

The team tackled the question of Himalayan human origins by sequencing the genomes of eight individuals from three cultural periods spanning 3,150 to 1,250 years before the present – from the earliest known human settlements to the establishment of the Tibetan Empire. These sequences were then compared with genetic samples from modern Himalayan dwellers.

Aldenderfer’s team collected the genetic specimens in Asia, then brought them to Warinner’s lab where the DNA was extracted. From there, the genomes were transported to the Di Rienzo lab at the University of Chicago for sequencing and analysis.

Anna Di Rienzo, of the department of human genetics at the University of Chicago, sequenced and analyzed these genomes on the Beagle supercomputer at the Computation Institute and the Tarbell cluster at the Center for Research Informatics. Sequencing and analysis clocked nearly 90,000 processor hours, occasionally using more than 800 processors at a time, she says.

Beagle

Among HPC Top500

212 teraFLOPS peak performance

728 compute nodes

46,464 GB total RAM

“While ancient DNA work in Europe has made enormous progress and has given new insights into the history of that part of the world, in Asia there is comparatively very little ancient DNA work published,” Di Rienzo points out.

“More than that, the Himalayas and the Tibetan plateau are very interesting in human evolution because: 1) they represent a major barrier to gene flow, and 2) habitation of these regions required major genetic adaptations. Thus ancient DNA can illuminate the history of migration and of adaptations.”

In sum, the analysis revealed a continuity between pre-historic and modern Himalayan humans. This is strong confirmation that the diverse material culture of ancient Himalayan humans is not the result of large-scale gene flow or population replacement from outside highland East Asia.

Perhaps most revealing is the fact that both prehistoric individuals and contemporary Tibetan populations share beneficial mutations in two genes implicated in adaptation to low-oxygen conditions found at high altitudes.

To solve the Himalayan mystery, this international team of scientists journeyed to the world’s highest points, to gather some of the oldest human genetic material. But the answer to the riddle only came after tapping into some of the world’s most powerful computers.

In this marriage of ancient and modern, high and low, near and far, this team of scientists demonstrate a model of contemporary computationally-enabled science, a model that promises to take us farther than we ever could have dreamed.

This work was supported by the US National Science Foundation, US National Institutes of Health, and the University of Chicago Comprehensive Cancer Center Support Grant, with particular support from the Genomics Core Facility, the National Geographic Society, the Henry Luce Foundation, Samsung Scholarship, The North Face and Field Museum.

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